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MolecRank: A Specificity-Based Network Analysis Algorithm

Ranking Therapeutic Molecules in the Bibliome
  • Ahmed Abdeen HamedEmail author
  • Agata Leszczynska
  • Mark Schreiber
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 921)

Abstract

Biomedical scientists often search databases of therapeutic molecules to answer a set of drug-related queries. In this paper, we present a novel network algorithm called MolecRank that is specialized in searching and ranking molecules using a biomedical literature. Starting with a disease-related set of publications (e.g., depression), a feature extraction step is performed to identify the biological features associated with the drugs of study. The MolecRank is a network centrality algorithm that is specialized in deriving a rank when specificity is in question. The algorithm’s promise is two folds (a) an interesting search-and-rank tool that demonstrated its importance in the drug discovery research, (b) a theoretical network centrality measure that is based on the notion of specificity. We performed our experiments against a depression-related literature dataset. The results shows an interesting order that is significantly different from well-advertised drugs (e.g., Cymbalta#10 though well-advertised). We conclude that not all well-advertised drugs are most specific. This striking evidence highlights the significance of specificity as an important measure in discovering new drugs.

Keywords

Specificity centrality Ranking algorithms Therapeutic molecules Literature mining 

Notes

Acknowledgement

The authors would like thank Greg Temsi, Ramiro Barrantes for their valuable discussions. The authors also greatly appreciate the tremendous feedback on this work giving by Dr. Barabasi and his lab members. We also thank Dr. Karin Verspoor of University of Melbourne for the valuable discussions.

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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Ahmed Abdeen Hamed
    • 1
    Email author
  • Agata Leszczynska
    • 2
  • Mark Schreiber
    • 1
    • 3
  1. 1.Merck & Co., Inc.BostonUSA
  2. 2.MSDPragueCzech Republic
  3. 3.Kaleido BiosciencesBedfordUSA

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